Mail opens on oldest messages

I use this format for viewing mail:

I am able to set the sort order on every mailbox so the newest (or latest) email is at the top.

If this is the format you're using give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

My solution is to keep my mail folders empty with the exception of the current day.

For me, if email data and attachments are worth keeping, I save the attachments to disk so they can easily be accessed on the drive as well as in the CCC backup set.

I save emails( less attachments) I feel are important in a separate folder, or folders, appropriately named in my Documents folder. Easy to access and they are also easily retrievable from the backup data sets.